rs4130140

Positions:

• chr17-407766-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_136407.1(LOC105371430):​n.331-3174C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,072 control chromosomes in the GnomAD database, including 2,510 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2510 hom., cov: 31)
• Consequence: LOC105371430 NR_136407.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.810

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371430	NR_136407.1	n.331-3174C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000466740.2	n.331-3174C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000599026.1	n.835+1431C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000629249.1	n.256-3141C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27108 AN: 151954 Hom.: 2504 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.0668

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.174

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.178 AC: 27138 AN: 152072 Hom.: 2510 Cov.: 31 AF XY: 0.177 AC XY: 13145 AN XY: 74310

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.0669

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.172

Alfa AF: 0.180 Hom.: 1525

Bravo AF: 0.177

Asia WGS AF: 0.163 AC: 569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.86

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4130140; hg19: chr17-257557;